Daxx depletion remodels silent rDNA chromatin and increases UBF-bound transcriptional potential

Ribosomal DNA (rDNA) repeats are regulated by DNA methylation, histone modifications, nucleosome occupancy, and nucleolar organization. Here, we used a data-driven ChIP-seq background-subtraction strategy to re-examine epigenetic profiles at rDNA repeats and found that Daxx and Atrx are preferentially enriched in the promoter and coding regions of silent rDNA. Daxx depletion in mouse embryonic fibroblasts reduced rDNA-associated H3K9me3 and DNA methylation, increased UBF occupancy, and shifted silent rDNA toward a transcription-permissive chromatin state. However, bulk rRNA transcription did not increase under basal MEF conditions, indicating that Daxx loss releases rDNA transcriptional potential rather than directly elevating rRNA output in all cellular contexts. In contrast, DAXX knockdown in the human glioblastoma cell line U87 enhanced rRNA transcription and nucleolar activity, indicating that the released rDNA transcriptional potential is converted into increased rRNA output in proliferating tumor cells. Analyses of TCGA-LGG and public cancer databases suggest that ATRX deficiency may contribute to enhanced ribosome-biogenesis signatures in glioma, whereas DAXX can also exert cancer-type-specific functions beyond the canonical ATRX/DAXX complex. These findings refine the role of Daxx as a regulator of silent rDNA chromatin and highlight rDNA chromatin remodeling as a potential link between repeat epigenetics, nucleolar activity, and tumor biology.